Most resume writing professionals advise against stapling your cover letter to your resume. (See Reference 3.) While it is important to keep both these documents together, generally an employer will read the cover letter and want to throw it away, keeping the resume if he plans to interview you.
If the cover letter and/or resume are more than a page, the whole package will appear quite unorganized. For a very professional look, consider presenting or mailing your cover letter and resume in a folder. If you have letters of recommendation, a portfolio of projects or other documents, those would go in first (meaning the last things that would be seen when opening the folder). Then place your resume, then the cover letter. You would either hand the folder to the employer or mail the package in a 9 by 12 inch envelope. Don’t fold it in thirds and stuff it into a small envelope. Be sure the heading of the cover letter is upright.
Staples vs. Paper Clips
If your resume is more than one page, some experts suggest that you can staple these together since it is really one document. You might consider paper-clipping them, especially if the second page includes only information such as education and degrees, since the employer may only be interested in your contact information and work history.